Isolated primate embryonic cells derived from extended blastocysts

ABSTRACT

An isolated primate embryonic cell is provided as well as cell cultures and cell lines derived therefrom. Also provided are methods of generating and using such cells.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No. 11/665,248 filed on Apr. 12, 2007, which is a National Phase of PCT Patent Application No. PCT/IL2005/001074 having International Filing Date of Oct. 11, 2005, which claims the benefit of priority of U.S. Provisional Patent Application No. 60/617,045 filed on Oct. 12, 2004. The contents of the above applications are all incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention relates to cells derived from delayed blastocysts and to cell lines generated therefrom.

Embryonic development starts soon after fertilization with blastomer cleavage, proliferation and differentiation. The blastomers within the developing mammalian embryo remain totipotent until the morula compaction stage. In the compacted embryo, the blastomers initiate polarization which results in two distinct cell-populations; the inner cell mass (ICM), which contributes to the embryo, and the outer trophectoderm layer, which develops into the extra embryonic layers. It is at this stage of embryogenesis—towards the end of the first week of development that embryonic stem (ES) cells are traditionally derived from the inner cell mass of the blastocyst.

At the time of implantation, the ICM is separated into a layer of primitive endoderm, which gives rise to the extra embryonic endoderm, and a layer of primitive ectoderm, which gives rise to the embryo proper and to some extra embryonic derivatives [Gardner J. Embryological Experiment and Morphology, 1982; 68: 175-198]. During the next major phase of development, termed gastrulation, the embryonic ectoderm differentiates into the three primary germ layers—endoderm (inside layer), mesoderm (middle layer), and ectoderm (outer layer). The cells become progressively restricted to a specific lineage, losing their pluripotency and thus are regarded as multi-potent progenitor cells. Therefore, pluripotent embryonic stem cells proliferate and replicate in the intact embryo only for a limited period of time.

Embryonic stem cells are characterized by their ability to propagate indefinitely in culture, as undifferentiated cells, while they can be induced to differentiate in vivo into teratomas when injected into SClD mice [Thomson, J. A., et al., (1998), Science, 282, 1145-1147; Reubinoff, B. E., et al., (2000), Nature Biotechnol., 18, 399-404]. They may also differentiate in vitro into embryoid bodies (EBs) that contain embryonic cells from the three germ layers (endoderm, mesoderm, and ectoderm). Moreover, this differentiation can be somewhat directed by the addition of growth factors into the culture media.

Human ES cells may also be genetically manipulated in culture [Eiges et al., (2001) Curr. Biol., 11, 514-518] and the transfected cells remain pluripotent and retain a normal karyotype [Shuldiner et al., (2003) Stem Cells 21, 257-265].

As a result of their unique features, it has been suggested that human ES cells hold the promise of changing the face of cell transplantation, by replacing or restoring tissue that has been damaged by disease or injury. Replacement of non-functional cells using ES cells technology can offer a lifelong treatment. Thus, diseases that might be treated by transplanting human ES-derived cells include Parkinson's disease, diabetes, traumatic spinal cord injury, Purkinje cell degeneration, Duchenne's muscular dystrophy, heart failure, and osteogenesis imperfecta.

Many other potential uses of human ES cells have been proposed that do not involve transplantation. For example, human ES cells could be used to study early events in human development. Human ES cells could also be used to test candidate therapeutic drugs or potential toxins by directing their differentiation into specific cell types. ES-derived cells may be more likely to mimic the in vivo response to the drug(s) being tested than animal and other in-vitro models and so offer safer, and potentially cheaper, models for drug screening.

Finally, human ES cells could be used to develop new methods for genetic engineering. Currently, the genetic complement of mouse ES cells in vitro can be modified easily by techniques such as homologous recombination. Using this method, genes to direct differentiation to a specific cell type or genes that express a desired protein product might be introduced into the ES cell line. Ultimately, if such techniques could be developed using human ES cells, it may be possible to devise better methods for gene therapy.

At present the only source for embryonic stem cells is the pre-implantation blastocyst embryo.

The pluripotency of human post-implantation embryonic cells between the time of implantation and the gastrulation process has as yet never been examined. Surani and Edwards teach in vitro culturing techniques of human embryos to day 9, demonstrating the presence of proliferating and healthy ICM [Edwards R. G., Surani M. A. H. (1978) Upsala Journal of Medical Sciences 22: 39-50].

However, they did not examine the pluripotency of stem cells at this post-implantation stage and did not isolate or culture them to allow their characterization.

Rathjen and colleagues teach a method for homogenous differentiation of mouse embryonic stem cells into early primitive ectoderm-like (EPL) using conditioned medium of Hep G2 cells [Rathjen et al. 1999, J. of Cells Science 112, 601-612] and demonstrate some similarities between them and the embryonic stem cells of the present invention. For example both cell types have a colony morphology of epithelial-like structures, a higher tendency to differentiate into mesodermal tissues and a reduced ability to either integrate into the embryonic germ layers after injection into mouse blastocysts [Lake et al. 2000, J. of Cells Science 113, 555-566] or form teratomas. However, in sharp contrast to the embryonic stem cells of the present invention, the EPLs unique features together with their ability to be cultured for limited passages in vitro are irreversible when the Hep G2 conditioned medium is removed [Rathjen et al. 1999 J. of Cells Science 112, 601-612; Lake et al. 2000, J. of Cells Science 113, 555-566]. The gene expression pattern of these cells is also different. The EPL cells, for example, express brachyury only as early EBs and not as undifferentiated cells like the embryonic stem cells of the present invention [Rathjen et al., 2000 J Cell Sci. 2000 113:555-66]. Together with the fact that the isolated EPLs are non-primate cells, the above mentioned differences indicate distinct cell populations.

The very broad range of potential applications for embryonic stem cells suggests that the identification of additional sources together with the novel stem cell lines derived therefrom, will be of critical importance for medical research in general and the advancement of stem cell research in particular.

SUMMARY OF THE INVENTION

According to one aspect of the present invention there is provided an isolated primate embryonic cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue.

According to another aspect of the present invention there is provided a cell culture comprising the isolated primate embryonic cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue.

According to yet another aspect of the present invention there is provided a method of generating a primate embryonic cell culture comprising providing a blastocyst of at least nine days post fertilization, isolating cells from the blastocyst; and culturing the isolated cells, thereby generating the primate embryonic cell culture.

According to still another aspect of the present invention there is provided a method of generating a primate embryonic cell line comprising providing a blastocyst of at least nine days post fertilization; isolating cells from the blastocyst; culturing the isolated cells; and cloning at least one of the isolated cells, thereby generating the primate embryonic cell line.

According to an additional aspect of the present invention there is provided a pharmaceutical composition comprising as an active ingredient a cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue and a pharmaceutically acceptable carrier.

According to yet an additional aspect of the present invention there is provided a method of treating or preventing a disease in which cell transplantation is therapeutically beneficial comprising inducing cell differentiation in the isolated human embryonic cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue and transplanting a therapeutically effective amount of the differentiated cells into a subject in need thereof, thereby preventing or treating a disease in which cell transplantation is therapeutically beneficial.

According to still an additional aspect of the present invention there is provided a method of generating a lineage specific cell comprising inducing a lineage-specific cell differentiation in the isolated primate embryonic cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue, thereby generating the lineage specific cell.

According to further features in preferred embodiments of the invention described below, the isolated primate embryonic cell further expresses at least one cartilage marker

According to still further features in the described preferred embodiments, the at least one cartilage marker is selected from the group consisting of COMP, aggrecan and collagen type II.

According to still further features in the described preferred embodiments, the cell culture further comprises feeder cells.

According to still further features in the described preferred embodiments, the cell culture, further comprises growth medium.

According to still further features in the described preferred embodiments, the providing the blastocyst is effected by ex-vivo culturing the blastocyst.

According to still further features in the described preferred embodiments, the ex-vivo culturing the blastocyst is effected on feeder cells.

According to still further features in the described preferred embodiments, the ex-vivo culturing the blastocyst is effected on a synthetic surface.

According to still further features in the described preferred embodiments, the culturing the isolated cells is effected on feeder cells.

According to still further features in the described preferred embodiments, the culturing the isolated cells is effected on a synthetic surface.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell maintains a stable normal karotype for at least one year.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell expresses SSEA4 and TRA-1-60 markers.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell does not express SSEA1 marker.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell expresses less TRA-1-81 marker than an embryonic stem cell of the same primate species not expressing brachyury using identical assay conditions.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell is capable of colony organization of columnar epithelium with villi throughout the upper side of the colony.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell has an OCT4 protein level lower than the OCT4 protein level in an embryonic stem cell of the same primate species not expressing brachycury using identical assay conditions.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell expresses more mesodermal differentiating markers than an embryonic stem cell of an identical primate not expressing brachyury using identical assay conditions.

According to still further features in the described preferred embodiments, the isolated primate cell is genetically modified.

According to still further features in the described preferred embodiments, the feeder cells are mouse feeder cells or human feeder cells.

According to still further features in the described preferred embodiments, the mouse feeder cells are mitotically inactivated mouse embryonic fibroblasts or primary mouse embryonic fibroblasts.

According to still further features in the described preferred embodiments, the human feeder cells are selected from the group comprising embryonic fibroblast cells, adult fallopian epithelial cells and foreskin cells.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell is in an undifferentiated proliferative state for at least 100 passages.

According to still further features in the described preferred embodiments, the isolated primate embryonic cell is immortalized.

According to still further features in the described preferred embodiments, the primate is a human.

According to still further features in the described preferred embodiments, the method of treating or preventing a disease in which cell transplantation is therapeutically beneficial further comprises genetically modifying the differentiated cell to express a therapeutic agent.

According to still further features in the described preferred embodiments, the inducing cell differentiation comprises genetically modifying a plurality of the cells.

The present invention successfully addresses the shortcomings of the presently known configurations by providing a

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

The invention is herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only, and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention, the description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.

In the drawings:

FIGS. 1A-E are photographs of light microscopy images depicting the generation of extended blastocyst cell lines (EBCs). FIGS. 1A-D depict the generation of the J3 cell line. FIG. 1A depicts an early blastocyst prior to plating on mouse embryonic feeder cells (MEFs). Hoffman resolution bar=120 μM. FIG. 1B depicts the identical human embryo following plating for five days on MEFs. Hoffman resolution bar=120 μM. FIG. 1C depicts the identical human embryo following plating for nine days on MEFs. Hoffman resolution bar=120 μM. FIG. 1D depicts the resulting EBC cells. Hoffman resolution bar=20 μM. FIG. 1E depicts an extended blastocyst cell line (J6) following a second passage for ten days on MEFs. The yellow line represents the outline of a condense area containing the stem cells. Hoffman resolution bar=135 μM.

FIGS. 2A-E are photographs of light (FIGS. 2A-C; Hoffman resolution bar=20 μM; H&E staining) and electron (2D-E; Hoffman resolution bar=8 μM) microscopy images depicting the organization of EBC and ESC colonies. FIG. 2A depicts the organization of an ESC colony I6. FIG. 2B depicts the organization of the EBC colony J3. FIG. 2C depicts the organization of the EBC colony J6. FIG. 2D depicts the organization of the pre-implantation cell line H9 as observed with electron microscopy. FIG. 2E depicts the organization of the EBC cell line J3 as observed with electron microscopy.

FIGS. 3A-G are a series of photographs depicting the fluorescent immunostaining with stage specific markers of EBCs and ESCs. FIG. 3A depicts J3 colony staining with SSEA4. FIGS. 3B and 3C depict DM-1 (an hESC line derived from ICM) staining with SSEA4 under a light (FIG. 3B) and fluorescent (3C) microscope. FIGS. 3D and 3E depict DM-1 staining with TRA-1-6 under a light (FIG. 3D) and fluorescent (FIG. 3E) microscope. FIGS. 3F and 3G depict WS-1 (an hESC line derived from ICM) staining with TRA-1-81 under a light (FIG. 3F) and fluorescent (FIG. 3G) microscope. Phase contrast Bar=50 μM.

FIGS. 4A-B are photographs of teratoma sections stained with hematoxylin/eosin (H&E) as observed under a light microscope. Hoffman resolution bar=20 μM. The teratomas were generated following introduction of cells from IS (FIG. 4A) and J2 (FIG. 4B) cell lines into four-week-old male SCID-beige mice.

FIGS. 5A-F are photographs of teratoma sections of EBC lines stained with H&E as observed under a light microscope demonstrating representative tissues of the three embryonic germ layers. The teratomas were generated following introduction of cells from J2 cell lines into four-week-old male SCID-beige mice. FIG. 5A depicts epithelium. Hoffman resolution bar=100 μM. FIG. 5B depicts secretory glands. Hoffman resolution bar=40 μM. FIG. 5C depicts fat tissue. Hoffman resolution bar=40 μM. FIG. 5D depicts mesenchymal tissue. Hoffman resolution bar=40 μM. FIG. 5E depicts bone tissue. Hoffman resolution bar=40 μM. FIG. 5F depicts myelinated nerve. Hoffman resolution bar=60 μM.

FIG. 6 is a photograph of a teratoma section of an EBD line stained with H&E showing cartilage and bone tissue as observed under a light microscope. The teratoma was generated following introduction of cells from J6 cell lines into four-week-old male SCID-beige mice. Hoffman resolution bar=20 μM.

FIG. 7 is a bar graph depicting the relative expression of October 4 according to quantitative real-time PCR analysis in I3, J3 and J6 cell line. NTC=no template control, i.e. samples where no cDNA was added. I3 was used as the calibrator=1 (100%).

FIGS. 8A-D are dot graphs and photographs from chip DNA analysis of the GEarray S series stem cells genes, Hs601.2. FIG. 8A is a dot graph comparing the gene expressions of two different hESC lines. FIG. 8B is a dot graph comparing the gene expressions of two different EBC cell lines. FIG. 8C is a dot graph comparing the average gene expression of hESC with EBC cell lines. FIG. 8D is a representative example of the chip.

FIGS. 9A-I are photographs of the J6 undifferentiated EBC cell line double stained with brachyury and Oct-4. FIGS. 9A, 9D and 9G depict brachyury staining alone. FIGS. 9C, 9F and 9I depict Oct-4 staining alone and FIGS. 9B, 9E and 9H depict the combined staining of both brachyury and Oct-4. Phase contrast bar=20 μM.

FIGS. 10A-I are photographs of the I3 hESC cell line double stained with brachyury and Oct-4. FIGS. 10A, 10D and 10G depict brachyury staining alone. FIGS. 10C, 10F and 10I depict Oct-4 staining alone and FIGS. 10B, 10E and 10H depict the combined staining of both brachyury and Oct-4. FIGS. 10A-C are of a differentiating colony of hESC lines; FIGS. 10D-F are of an undifferentiated colony of hESC line; FIGS. 10G-I are of an undifferentiated colony of hESC line. Phase contrast bar=20 μM.

FIGS. 11A-B are computer generated images following bioinformatic analysis using the MAS 5.0 Affymetrix array analysis software of four Affymetric focus gene chips hybridized with cDNA from four cell lines (I3, I6 J3 and J6). FIG. 11A is a dendrogram based on the similarity between the four tested lines (I3, I6 J3 and J6). The following calculation settings were used: Columns included: J6 Signal, Z Scores, I3 Signal, Z Scores, I6 Signal, Z Scores, J3 Signal, Z Scores; Empty values replaced by: 0; Clustering method: Complete linkage (maximum); Similarity measure: Correlation; Ordering function: Average value. FIG. 11B is a heat map of the 238 probe sets which were significantly different in I cell lines and the J cell lines with a maximum p-value of 0.05.

FIG. 12 is a pie chart illustrating the results obtained following Go-Chat analysis of the 238 probe sets which were significantly different in I cell lines and the J cell lines with a maximum p-value of 0.05.

FIGS. 13A-F are photographs of two-dimensional gel electrophoresis of an area within the gel that clearly differs between 5-day old EBs and undifferentiated hESCs. All treatments were performed on cells from the I4 cell line. FIG. 13A is a photograph of the Master gel (i.e. a gel on which MEF protein extract alone has been run) following two-dimensional gel electrophoresis. FIG. 13B is a photograph of two-dimensional gel electrophoresis of MEFs used to culture the hESCs. FIG. 13C is a duplicate of 13B. FIG. 13D is a photograph of two-dimensional gel electrophoresis of undifferentiated hESCs. FIG. 13E is a photograph of two-dimensional gel electrophoresis of hESCs that were cultured for 10 days as monolayers. FIG. 13F is a photograph of two-dimensional gel electrophoresis of 5-days old EBs.

FIGS. 14A-F are photographs of two-dimensional gel electrophoresis demonstrating an area within the gel that clearly differs between differentiated hESCs and undifferentiated hESCs. All treatments are performed on cells from the I4 cell line. FIG. 14A is a photograph of the Master gel following two-dimensional gel electrophoresis. FIG. 14B is a photograph of two-dimensional gel electrophoresis of MEFs used to culture the hESCs. FIG. 13C is a duplicate of 14B. FIG. 14D is a photograph of two-dimensional gel electrophoresis of undifferentiated hESCs. FIG. 14E is a photograph of two-dimensional gel electrophoresis of hESCs that were cultured for 10 days as monolayers. FIG. 14F is a photograph of two-dimensional gel electrophoresis of differentiated hESCs.

FIGS. 15A-B are photographs of Alizarin Red stained EB derived cells (EBDs). FIG. 15A depicts EBDs resulted from I4 (hESC) cells and FIG. 15B depicts EBDs from J6 cells (DBC) treated with the same medium supplemented with TGF_(β3). While the hESC demonstrated no positive staining the DBC cells demonstrated large area of clear red staining. FIG. 15A: Bar=15 μM and FIG. 15B: Bar=50 μM.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is of isolated primate embryonic stem cells and methods of generating stem cell cultures and cell lines therefrom. Specifically, the present invention relates to isolated embryonic stem cells which are characterized by expression of brachyury and their ability to differentiate to derivatives of endoderm, mesoderm, and ectoderm tissues.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.

Embryonic stem cells are characterized by their ability to propagate indefinitely in culture, as undifferentiated cells, while they can be induced to differentiate in vivo into teratomas when injected into SClD mice [Thomson, J. A., et al., (1998), Science, 282, 1145-1147; Reubinoff, B. E., et al., (2000), Nature Biotechnol., 18, 399-404]. They may also differentiate in vitro into embryoid bodies (EBs) that contain embryonic cells from the three germ layers (endoderm, mesoderm, and ectoderm) [Itskovitz-Eldor, J. et al., Mol. Med., 6, 88-95]. Moreover, this differentiation can be somewhat directed by the addition of growth factors into the culture media [Schuldiner, M et al., (2000) P.N.A.S. USA, 97, 11307-11312]. For example, ES cells can be induced to differentiate in vitro into cardiomyocytes [Paquin et al., Proc. Nat. Acad. Sci. (2002) 99:9550-9555], hematopoietic cells [Weiss et al., Hematol. Oncol. Clin. N. Amer. (1997) 11(6):1185-98; U.S. Pat. No. 6,280,718], insulin-secreting beta cells [Assady et al., Diabetes (2001) 50(8):1691-1697], and neural progenitors capable of differentiating into astrocytes, oligodendrocytes, and mature neurons [Reubinoff et al., Nature Biotechnology (2001) 19:1134-1140; U.S. Pat. No. 5,851,832].

Human ES cells may also be genetically manipulated in culture [Eiges et al., (2001) Curr. Biol., 11, 514-518] and the transfected cells remain pluripotent (i.e., capable through its progeny of giving rise in vivo to all the cell types which comprise the adult animal including the germ cells) and retain a normal karyotype [Shuldiner et al., (2003) Stem Cells 21, 257-265].

As a result of their unique features, it has been suggested that human ES cells hold the promise of changing the face of cell transplantation, by replacing or restoring tissue that has been damaged by disease or injury. Replacement of non-functional cells using ES cells technology can offer a lifelong treatment. Thus, diseases that might be treated by transplanting human ES-derived cells include Parkinson's disease, diabetes, traumatic spinal cord injury, Purkinje cell degeneration, Duchenne's muscular dystrophy, heart failure, and osteogenesis imperfecta.

ESCs have been successfully isolated from primates (Thomson et al., 1998 Science, 282, 1145-1147; Amit et al., 2000 Dev. Biol. 227: 271-8), mice (Mills and Bradley, 2001, Trends Genet. 17: 331-9) and other species where they are derived from the inner cell mass (ICM) of the mammalian blastocyst prior to the implantation stage.

Whilst reducing the present invention to practice, the present inventors have uncovered that human embryonic stem cells may be derived from a post-implantation stage blastocyst. Moreover these stem cells display different characteristics to the traditional embryonic stem cells derived from pre-implantation stage blastocysts while are still capable of differentiating to all the cell types which comprise the adult animal (Example 3, FIGS. 4A-B and 5A-F) and therefore represent a novel class of embryonic stem cell.

Thus, as described in the Examples section which follows embryonic stem cells derived from post-implantation/pre-gastrulation stage blastocysts [referred to herein as extended blastocyst cells (EBCs)] display a different colony morphology (FIGS. 2A-E) and express different levels of both cell surface markers and differentiation markers to ESCs derived from pre-implantation stage blastocysts. Specifically, EBCs express many early differentiation markers, mostly mesodermal, as demonstrated by RT-PCR (Table 3, Example 3 and FIG. 7), histochemistry (FIGS. 3A-X, 9A-I and 10A-I), two-dimensional gel electrophoresis (FIGS. 13A-F and 14A-F) and chip DNA analysis (FIGS. 8A-D, 11A-B and 12).

It will be appreciated that although ex vivo culturing of human embryos until day 9 has been previously reported, the prior art does not teach of stem cell isolation or culturing. Moreover, the pluripotency of these stem cells at this post-implantation stage was not examined [Edwards R. G., Surani M. A. H. (1978) Upsala Journal of Medical Sciences 22: 39-50].

Thus, according to one aspect of the present invention there is provided an isolated primate embryonic cell characterized by expression of brachyury and ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue.

As used herein the phrase “primate embryonic cell” refers to a cell from embryonic primate origin. Typically the embryonic cell of this aspect of the present invention has a high nuclear/cytoplasmic ratio and prominent nucleolus.

As used herein the term “primate” refers to both higher and lower primates. Preferably the primate is a human.

According to this aspect of the present invention, the term “isolated” refers to an embryonic cell or a plurality of embryonic cells that have been removed from their naturally-occurring in-vivo environment (i.e. post-implantation/pre-gastrulation stage blastocyst). Preferably the isolated embryonic cell of this aspect of the present invention (i.e., expressing Brachyury and being capable of differentiating to derivatives of each of an endoderm, mesoderm, and ectoderm tissue) is substantially free from other substances (e.g., other cells, proteins, nucleic acids, etc.) that are present in its in-vivo environment. Methods for removing embryonic cells from a post-implantation/pre-gastrulation stage blastocyst are described hereinbelow and in the Examples section which follows.

As used herein, the term “brachyury” refers to the human T-box transcription factor, of Swiss Prot No. 015178 and homologues and orthologues thereof, such as encoded by the polynucleotide sequences listed in Table 1 below.

TABLE 1 Species GenBank Accession Number Chimpanzee 472186 Chimpanzee XM_527563.1 Chimpanzee XP_527563.1

As used herein, the phrase “expression of brachyury” refers to mRNA/protein expression of brachyury. Preferably, the endogenous expression of Brachyury in the isolated cells of the present invention is at least two times higher, preferably at least five times higher and more preferably at least ten times higher than the endogenous expression of Brachyury protein in embryonic stem cells derived from pre-implantation blastocysts. Increased expression of Brachyury protein may be confirmed using standard techniques known in the art further described hereinbelow.

As used herein, the phrase “derivatives of each of an endoderm, mesoderm and ectoderm tissue” encompasses fully or partially differentiated cells. This characteristic of the cells of the present invention resembles the ability of embryonic stem cells to derivatives of each of an endoderm, mesoderm and ectoderm tissue. Examples of endoderm derivatives include, but are not limited to, hepatocytes and pancreatic cells. Examples of mesoderm derivatives, include but are not limited to, osseous, cartilaginous, elastic, fibrous connective tissues, myocytes, myocardial cells, bone marrow cells, vascular cells (namely endothelial and smooth muscle cells), and hematopoietic cells. Examples of ectoderm derivatives include but are not limited to neural, retina and epidermal cells.

The isolated primate embryonic cells of the present invention may be obtained from a blastocyst of at least nine days post fertilization at a stage prior to gastrulation. Blastocysts less than nine days old may be obtained from in vivo preimplantation embryos, in vitro fertilized (IVF) embryos or from single cell embryos expanded to the blastocyst stage. Prior to culturing the blastocyst, the zona pellucida is digested (for example by Tyrode's acidic solution (Sigma Aldrich, St Louis, Mo., USA)) so as to expose the inner cell mass. The blastocysts are then cultured as whole embryos for at least nine and no more than fourteen days post fertilization (i.e. prior to the gastrulation event) in vitro using standard embryonic stem cell culturing methods.

Blastocyst culturing may be effected using currently practiced ES culturing methods. These are mainly based on the use of feeder cell layers which secrete factors needed for stem cell proliferation, while at the same time, inhibit their differentiation. Feeder cell-free systems have also been used in ES cell culturing, such systems utilize matrices supplemented with serum, cytokines and growth factors as a replacement for the feeder cell layer. The following summarizes culturing techniques which may be used in each of the steps of generating the embryonic cells of the present invention (also referred to as embryonic stem cells of the present invention). Currently preferred configuration of blastocyst culturing is described in Example 1 of the Examples section which follows.

Feeder-Layer Based Cultures

Mouse feeder layers—The most common method for culturing ES cells is based on mouse embryonic fibroblasts (MEF) as a feeder cell layer supplemented with tissue culture medium containing serum or leukemia inhibitor factor (LIF) which supports the proliferation and the pluripotency of the ES cells [Thomson J A, Itskovitz-Eldor J, Shapiro S S, Waknitz M A, Swiergiel J J, Marshall V S, Jones J M. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282: 1145-7; Reubinoff B E, Pera M F, Fong C, Trounson A, Bongso A. (2000). Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol. 18: 399-404]. MEF cells are derived from day 12-13 mouse embryos in medium supplemented with fetal bovine serum. Under these conditions mouse ES cells can be maintained in culture as pluripotent stem cells, preserving their phenotypical and functional characteristics. However, unlike mouse ES cells, the presence of exogenously added LIF does not prevent differentiation of human ES cells [Thomson J A, Itskovitz-Eldor J, Shapiro S S, Waknitz M A, Swiergiel J J, Marshall V S, Jones J M. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282: 1145-7; Reubinoff B E, Pera M F, Fong C, Trounson A, Bongso A. (2000). Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol. 18: 399-404]. Furthermore, the use of feeder cells substantially increases the cost of production, and makes scale-up of human ES cell culture impractical. Additionally, the feeder cells are metabolically inactivated to keep them from outgrowing the stem cells; hence it is necessary to have fresh feeder cells for each splitting of human ES culture. Since at present, the separation of feeder cell components from embryonic cells prepared in bulk culture cannot be efficiently achieved, feeder cell layer-prepared ES cultures are not suitable for human therapy.

ES cells can also be cultured on MEF under serum-free conditions using serum replacement supplemented with basic fibroblast growth factor (bFGF) [Amit M, Carpenter M K, Inokuma M S, Chiu C P, Harris C P, Waknitz M A, Itskovitz-Eldor J, Thomson J A. (2000). Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture. Dev. Biol. 227: 271-8]. Under these conditions the cloning efficiency of ES cells is 4 times higher than under fetal bovine serum. In addition, following 6 months of culturing under serum replacement the ES cells still maintain their pluripotency as indicated by their ability to form teratomas which contain all three embryonic germ layers. Although this system uses a better-defined culture conditions, the presence of mouse cells in the culture exposes the human culture to pathogens which restricts their use in cell-based therapy.

Human embryonic fibroblasts or adult fallopian epithelial cells as feeder cell layers—Human ES cells can be grown and maintained using human embryonic fibroblasts or adult fallopian epithelial cells. When grown on these human feeder cells the human ES cells exhibit normal karyotypes, present alkaline phosphatase activity, express Oct-4 and other embryonic cell surface markers including SSEA-3, SSEA-4, TRA-1-60, and GCTM-2, form teratomas in vivo, and retain all key morphological characteristics [Richards M, Fong C Y, Chan W K, Wong P C, Bongso A. (2002). Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cells. Nat. Biotechnol. 20: 933-6]. However, the major disadvantage of using human embryonic fibroblasts or adult fallopian tube epithelial cells as feeder cells is that both of these cell lines have a limited passage capacity of only 8-10 times, thereby limiting the ability of a prolonged ES growth period. For a prolonged culturing period, the ES cells must be grown on human feeder cells originated from several subjects which results in an increased variability in culture conditions.

Foreskin feeder layers—Human ES cells can be cultured on human foreskin feeder layer as disclosed in U.S. patent application Ser. No. 10/368,045. Foreskin derived feeder cell layers consist of a complete animal-free environment suitable for culturing human ES cells. In addition, foreskin cells can be maintained in culture for as long as 42 passages since their derivation, providing the ES cells with a relatively constant environment. Under these conditions the human ES cells were found to be functionally indistinct from cells grown with alternate protocols (e.g., MEF). Following differentiation, ES cells expressed genes associated with all three embryonal germ layers, in vitro, and formed teratomas in vivo, consisting of tissue arising from all three germ layers. In addition, unlike human fallopian epithelial cells or human embryonic fibroblasts, human ES cells cultured on foreskin feeder layers were maintained in culture in a pluripotent and undifferentiated state for at least 87 passages. However, although foreskin cells can be maintained in culture for long periods (i.e., 42 passages), the foreskin culture system is not well-defined due to differences between separate batches. In addition, human feeder layer-based culture systems would still require the simultaneous growth of both feeder layers and hES cells. Therefore, feeder-free culturing systems have been developed.

Feeder-Free Cultures

Stem cells can be grown on a solid surface such as an extracellular matrix (e.g., Matrigel® or laminin) in the presence of a culture medium. Unlike feeder-based cultures which require the simultaneous growth of feeder cells and stem cells and which may result in mixed cell populations, stem cells grown on feeder-free systems are easily separated from the surface. The culture medium used for growing the stem cells contains factors that effectively inhibit differentiation and promote their growth such as MEF-conditioned medium and bFGF. However, commonly used feeder-free culturing systems utilize an animal-based matrix (e.g., Matrigel®) supplemented with mouse or bovine serum, or with MEF conditioned medium [Xu C, et al. (2001). Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol. 19: 971-4] which present the risk of animal pathogen cross-transfer to the human ES cells, thus compromising future clinical applications.

The embryonic stem cells of the present invention can be isolated by virtue of their morphology (e.g. small cell with large nucleus) and/or by any other stem cell distinguishing feature. Isolation may be achieved by chemical or mechanical means or both. Preferably mechanical isolation and removal by a micropipette is used. Mechanical isolation may be combined with a chemical or enzymatic treatment to aid with dissociation of the cells, such as Ca²⁺/Mg²⁺free PBS medium or dispase.

The isolated embryonic stem cells of this invention may be cultured in any way which ensures their non-differentiated state as described hereinabove. An exemplary culturing medium comprises 85% ko-DMEM and supplemented with 15% ko-serum replacement, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% non-essential amino acid stock and 4 ng/ml basic fibroblast growth factor (bFGF) (all products from Gibco Invitrogen corporation products, San Diago, Calif., USA). Methods of qualifying the embryonic stem cells of the present invention are well known in the art. For example, differentiation state may be determined by injecting cells into a 8-12 week old SCID mice (FIGS. 5A-F) as described by Evans et al., [Evans M J and Kaufman M (1983) Cancer Surv. 2: 185-208], which upon injection form teratomas. Teratomas are typically fixed using 4% paraformaldehyde and histologically examined for the three germ layers. Alternatively, this can be confirmed by determining their ability to form embryonal bodies as described in Example 3 of the Examples section which follows.

The embryonic stem cells of the present invention can also be qualified by the expression of cell markers. Typically, expression of cell markers can be detected using a variety of cell biology, molecular biology and biochemical techniques which are well known in the art. For example flow cytometry may be used to detect membrane-bound markers, immunohistochemistry may be used to detect intracellular markers, and enzyme-linked immunoassays may be used to detect markers secreted into the medium. The expression of protein markers can also be detected at the mRNA level by reverse transcriptase-PCR (using marker-specific primers), Northern blots and oligonucleotide microarrays.

Thus, the embryonic stem cells of the present invention may be qualified by the expression of stage-specific embryonic antigens (SSEA). Antibodies for SSEA markers are available from the Developmental Studies Hybridoma Bank (Bethesda Md.). Other markers which are typically used for the qualification of embryonic stem cells are Tra-1-60 and Tra-1-81 (antibodies available from Chemicon International, Temecula, Canada) and Octamer binding transcription factor 4 (OCT-4) (Santa Cruz). OCT-4 (GenBank Accession No. NM_(—)00270) is a member of the POU family of transcription factors. OCT-4 transcription is activated between the 4 and 80 cell stage in the developing embryo, and it is highly expressed in the expanding blastocyst and then in the pluripotent cells of the egg cylinder. Transcription is down-regulated as the primitive ectoderm differentiates to form mesoderm, and by 8.5 days post coitum is restricted to migrating primordial germ cells. Similar to embryonic stem cells not expressing brachyury, the embryonic stem cells of the present invention express SSEA4 and TRA-1-60 markers. However, in contrast to embryonic stem cells not expressing brachyury, the embryonic stem cells of the present invention do not express SSEA1 marker. In addition, the embryonic stem cells of the present invention express less TRA-1-81 and OCT-4 marker than embryonic stem cells not expressing brachyury using identical assay conditions.

The isolated primate embryonic stem cell of the present invention typically expresses more mesodermal differentiating markers than an embryonic stem cell of an identical primate not expressing brachyury. Typically, the isolated primate embryonic stem cells of the present invention express cartilage markers. Examples of cartilage markers which are expressed by the cells of the present invention include but are not limited to COMP (GenBank Accession No. L32137), aggrecan (GenBank Accession No. X17406) and collagen type II (GenBank Accession No. X06268).

Examples of other mesodermal differentiating markers that are expressed at a higher level in the embryonic stem cells of the present invention include, but are not limited to cartilage link protein (GenBank Accession No. U43328), cardiac actin (GenBank Accession No. NM_(—)005159), BMP4 (GenBank Accession No. D30751) and BMP2 (GenBank Accession No. NM_(—)001200).

Another method of qualification of embryonic stem cells is based on genetic analysis. Karotyping is one type of morphological analysis routinely performed for the qualification of embryonic stem cells. It is important in order to verify cytological euploidity, wherein all chromosomes are present and not detectably altered during culturing. Cultured stem cells can be karyotyped using a standard Giemsa staining and compared to published karyotypes of the corresponding species.

As is illustrated in Example 2 of the Examples section below, embryonic stem cells of the present invention retain a normal karyotype following at least twenty passages.

Microscopy is a type of morphological analysis routinely performed for the qualification of embryonic stem cells.

As demonstrated in Example 2 (FIGS. 2A-E) the isolated primate embryonic stem cells of the present invention are capable of a colony organization of columnar epithelium with villi throughout the upper side of the colony. Typically the colonies of embryonic stem cells not expressing brachyury are organized as stratified epithelium, with no villi facing the upper side (FIG. 2A). Furthermore, electron microscopy indicated that zonula occludente junctions, typical for columnar epithelium, could be detected between the embryonic stem cells of the present invention and not between the upper rows of embryonic stem cells not expressing brachyury (FIGS. 2D-E).

Preferably, the embryonic stem cells of the present invention remain in an undifferentiated proliferative state for at least 20, 30, 40, 50, 60, 70, 80, 90, preferably at least one hundred passages.

Stem cells generated according to the teachings of the present invention may be cultured on feeder cells or in a xenofree environment such as in the presence of synthetic extracellular matrix components (e.g., Matrigel™) as described above.

An isolated embryonic stem cell may be cloned from the culture described hereinabove in order to generate an embryonic stem cell line. Methods of cloning are well known in the art.

Cell lines of the present invention can be produced by immortalizing the cloned cells by methods known in the art, including, for example, expressing a telomerase gene in the cells (Wei, W. et al., 2003. Abolition of Cyclin-Dependent Kinase Inhibitor p16Ink4a and p21Cip1/Waf1 Functions Permits Ras-Induced Anchorage-Independent Growth in Telomerase-Immortalized Human Fibroblasts. Mol Cell Biol. 23: 2859-2870) or co-culturing the cells with NIH 3T3 hph-HOX11 retroviral producer cells (Hawley, R. G. et al., 1994. The HOX11 homeobox-containing gene of human leukemia immortalizes murine hematopoietic precursors. Oncogene 9: 1-12).

The embryonic stem cells may be further genetically modified at any stage of isolation. For example, they may be genetically modified through introduction of vectors expressing a selectable marker under the control of a stem cell specific promoter such as Oct-4. Some differentiated progeny of embryonic stem cells may produce products which are inhibitory to stem cell renewal or survival. Therefore selection against such differentiated cells, facilitated by the introduction of a construct such as that described above, may promote stem cell growth and prevent differentiation. The stem cells may be genetically modified at any stage with markers so that the markers are carried through to any stage of cultivation. The markers may be used to purify the differentiated or undifferentiated stem cell population at any stage of cultivation.

Alternatively, the embryonic stem cells of the present invention may be genetically modified to express a therapeutic agent or to direct differentiation into a specific cell lineage.

Various methods can be used to introduce an exogenous gene (e.g. the telomerase gene) in primate embryonic stem cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et al. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.

Introduction of nucleic acids by viral infection offers several advantages over other methods such as lipofection and electroporation, since higher transfection efficiency can be obtained due to the infectious nature of viruses.

The embryonic stem cells derived according to the teachings of the present invention can be used for several commercial and research applications.

Cultured embryonic stem cells of the present invention can be differentiated into restricted developmental lineage cells, or terminally differentiated cells.

Differentiation of stem cells can be initiated by allowing overgrowth of undifferentiated human ES cells in suspension culture forming embryoid bodies or by plating ES cells under conditions that promote differentiation in a particular manner. Such conditions may include withdrawing or adding nutrients, growth factors or cytokines to the medium, changing the oxygen pressure, or altering the substrate on the culture surface. For example, embryonic stem cells can be induced to differentiate in vitro into cardiomyocytes [Paquin et al., Proc. Nat. Acad. Sci. (2002) 99:9550-9555]. Several factors alone or in combination have been shown to enrich cardiac differentiation such as hepatocyte growth factor (HGF), epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), transforming growth factor β1 (TGF β1), platelet derived growth factor (PDGF), sphingosine-1 -phosphate, retinoic acid, 5-azacytidine and vitamin C. Embryonic stem cells have also been induced to differentiate into neural or glial lineages [Reubinoff et al., Nature Biotechnology (2001) 19:1134-1140; U.S. Pat. No. 5,851,832]. For their generation, the medium typically includes any of the following factors or medium constituents in an effective combination: Brain derived neurotrophic factor (BDNF), neutrotrophin-3 (NT-3), NT-4, epidermal growth factor (EGF), ciliary neurotrophic factor (CNTF), nerve growth factor (NGF), retinoic acid (RA), sonic hedgehog, FGF-8, ascorbic acid, forskolin, fetal bovine serum (FBS), and bone morphogenic proteins (BMPs). Embryonic stem cells have also been induced to differentiate into hematopoietic cells [Weiss et al., Hematol. Oncol. Clin. N. Amer. (1997) 11(6):1185-98; U.S. Pat. No. 6,280,718] and insulin-secreting beta cells [Assady et al., Diabetes (2001) 50(8):1691-1697].

Differentiation of stem cells can also be directed by genetic modification. Several transcription factors have been demonstrated to regulate differentiation of ES cells to specific cell types [Levinson-Dushnik M., Benvenisty N., Cell Biol. 17: 3817-3822, 1997]. Ectopic over-expression of such factors stimulates ES cells to differentiate selectively into certain cell types. For example over-expression of the transcription factor GATA-4 was shown to induce cardiomyocyte differentiation [Grepin C., et al., Development 124: 2387-2395, 1997; Fujikura J., et al., Genes Dev. 16: 784-789, 2002; Kanda S., et al., Hepatol. Res. 26:225-231, 2003]. Techniques for the genetic modification of the present invention are described herein above.

Alternatively, the embryonic stem cells of the present invention may be seeded over a porous scaffold (e.g. an alignate scaffold) as described in U.S. Pat. Appl. No. 60/604,002 to allow the formation of embryoid bodies (EBs) thereby allowing partial differentiation. The three dimensional scaffolds may be coated with components of extracellular matrix such as fibronectin, laminin, collagen and/or supplemented with cytokines, growth factors and chemokines. Cell seeding is effected in a manner which enables even distribution of the cells on/within the scaffold. One approach which can be utilized to achieve even distribution is seeding under a centrifugal force (Dar et al., 2002, Biotechnol Bioeng 80:305-312). Cells are preferably seeded at a concentration which ensures entrapment within the scaffold and maximal formation of EBs preferably about 5×10⁷ cells per cm³ scaffold. The embryoid bodies may be further differentiated along specific cell lineages as described hereinabove.

Since the cells of the present invention may be differentiated in a lineage specific fashion, they may be used for human cell-based therapy and tissue regeneration.

Thus, according to another aspect of the present invention there is provided a method of treating a disease in which cell transplantation is therapeutically beneficial.

The method according to this aspect of the present invention is effected by inducing cell differentiation in the isolated human embryonic stem cell of the present invention and transplanting a therapeutically effective amount of the differentiated cells into a subject in need thereof, thereby preventing or treating a disease in which cell transplantation is therapeutically beneficial.

As used herein “a disease in which cell transplantation is therapeutically beneficial” refers a disease, conditions or disorder such as a neurological disorder (e.g. Parkinson's disease), a muscular disorder (e.g. muscular dystrophy), a cardiovascular disorder (e.g. heart failure), an hematological disorder (e.g. leukemia, lymphoma, thalassemia and sickle cell anemia), a metabolic disorder (e.g. Type I diabetes), a skin disorder (e.g. psoriasis), a liver disorder (e.g. acute liver failure) that may be treated by cell transplantation.

The phrase “treating” refers to inhibiting or arresting the development of a disease, disorder or condition and/or causing the reduction, remission, or regression of a disease, disorder or condition in an individual suffering from, or diagnosed with, the disease, disorder or condition. Those of skill in the art will be aware of various methodologies and assays which can be used to assess the development of a disease, disorder or condition, and similarly, various methodologies and assays which can be used to assess the reduction, remission or regression of a disease, disorder or condition.

As used herein, “transplanting” refers to a means for providing the differentiated embryonic stem cells of the present invention, using any suitable route, e.g., oral, sublingual intravenous, subcutaneous, transcutaneous, intramuscular, intracutaneous, intrathecal, intra peritoneal, intra spleenic, intra hepatic, intra pancreatic, intra cardiac, epidural, intraoccular, intracranial, inhalation, rectal, vaginal, and the like. Cells may be transplanted as are or attached to a scaffold (matrix). Differentiation of the stem cells of the present invention may require specific environments for differentiation, which include the presence of a supporting scaffold (e.g. osteoblasts) The 3D scaffold provides a supporting frame and may act as a template for osteogenesis.

Differentiated embryonic stem cells of the present invention can be utilized in treating various disorders. For example, oligodendrocyte precursors can be used to treat myelin disorders (Repair of myelin disease: Strategies and progress in animal models. Molecular Medicine Today. 1997, 554-561), chondrocytes or mesenchymal cells can be used in treatment of bone and cartilage defects (U.S. Pat. No. 4,642,120) and cells of the epithelial lineage can be used in skin regeneration of a wound or burn (U.S. Pat. No. 5,716,411).

For certain disorders, such as genetic disorders in which a specific gene product is missing [e.g., lack of the CFTR gene-product in cystic fibrosis patients (Davies J C, 2002. New therapeutic approaches for cystic fibrosis lung disease. J. R. Soc. Med. 95 Suppl 41:58-67)], the embryonic stem cells of the present invention are preferably manipulated to over-express the mutated gene prior to their administration to the individual. It will be appreciated that for other disorders, the ESCs of the present invention should be manipulated to exclude certain genes.

Preferably, the embryonic stem cells of the present invention are at least partially differentiated prior to transformation as implantation of undifferentiated ES cells may lead to formation of benign teratomas in the recipients. This may be achieved by designing a transgenic methodology to eliminate residual minority stem cells from differentiated ES cell cultures, for example based on negative selection of Oct 4-expressing cells. Use of a positive selection transgene to achieve lineage-directed differentiation would also reduce the risk of tumor formation by selecting against the remaining undifferentiated, proliferating stem cell population.

The embryonic stem cells of the present invention may be genetically engineered (such as by using the above teachings) to reduce or eliminate immune-mediated rejection so that lifelong pharmacologic immunosuppression would not be required.

Homologous recombination has been used to “knock-out” major histocompatibility complex (MHC) class I and class II molecules in mouse ES cells [Grusby M J, et al., Proc Natl Acad Sci USA 1993;90:3913-3917]. However, MHC class I- and class II-deficient skin grafts are still rejected, possibly on the basis of indirect allo-recognition-mediated rejection and/or natural killer cell-mediated destruction [Grusby M J, et al., Proc Natl Acad Sci USA 1993;90:3913-3917]. Thus, in addition to deleting foreign MHC genes, desired MHC genes may also be “knocked-in”, so that ES cell-derivative transplants of the present invention are seen as “self” by the prospective recipient [Westphal C H, Leder P. Curr Biol 1997;7:530-533]. Alternatively, genes for immunosuppressive molecules such as Fas-ligand could be inserted into the ES cells of the present invention, or important immune-stimulating proteins, such as B7 antigens or CD40-ligand, could be deleted from ES cells [Harlan D M, Kirk A D, JAMA 1999;282:1076-1082]. Irrespective of the method used, the ability to stably integrate genetic modifications into ES cells provides an advantage over using adult somatic cells, which are less reliably genetically altered.

Nuclear transfer technology may provide a more precise means to prevent rejection of the transplanted ES cells of the present invention. This technique would lead to ES cell-derived cells that are an exact genetic match to the recipient. In this way, there would be minimal host immune response since all nuclear genes, including major and minor histocompatibility loci, would be seen as “self.”

In this technique, a nucleus is extracted from a normal somatic cell of a patient, e.g. from a skin biopsy, and then injected into an enucleated oocyte. Oocyte cytoplasm has the ability to reprogram differentiated nuclei, and as such, would reestablish an embryonic gene expression program in the chromatin of the somatic cell nucleus. A delayed blastocyst developing from this oocyte would be a source for the derivation of a new ES cell line of the present invention, which would be genetically matched for each nuclear gene of the patient. In this setting, the potential immune-mediated destruction of the graft would be limited to minor antigen differences derived from mitochondrial genes or to autoimmune processes, such as diabetes. Combining nuclear transfer technology and ES cell derivation has been successfully achieved in cows and mice, in order to establish transgenic ES cell lines from reprogrammed somatic cell nuclei [First NL, Thomson J., Nat Biotechnol 1998;16:620-621].

Establishing hematopoietic chimerism is another potential means of preventing rejection of the transplanted cells of the present invention. By using the same ES cell lines to derive both hematopoietic stem cells and other lineages, it may be possible to initially achieve hematopoietic chimerism followed by engraftment of a second cell type. The second lineage would not be rejected as it would be regarded as “self” by the chimeric patient's bone marrow and immune system, which were derived, in part, from the same ES cell line. No long-term treatment with potentially toxic drugs would then be required.

The embryonic stem cells of the present invention may be transplanted to a human subject per se, or in a pharmaceutical composition where it is mixed with suitable carriers or excipients.

As used herein a “pharmaceutical composition” refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of a compound to an organism.

Herein the term “active ingredient” refers to the embryonic stem cells of the present invention accountable for the biological effect.

Hereinafter, the phrases “physiologically acceptable carrier” and “pharmaceutically acceptable carrier” which may be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound. An adjuvant is included under these phrases.

Herein the term “excipient” refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.

Techniques for formulation and administration of drugs may be found in “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., latest edition, which is incorporated herein by reference.

One may administer the pharmaceutical composition in a systemic manner (as detailed hereinabove). Alternatively, one may administer the pharmaceutical composition locally, for example, via injection of the pharmaceutical composition directly into a tissue region of a patient.

Pharmaceutical compositions of the present invention may be manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.

Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.

For injection, the active ingredients of the pharmaceutical composition may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

For oral administration, the pharmaceutical composition can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the pharmaceutical composition to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for oral ingestion by a patient. Pharmacological preparations for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, titanium dioxide, lacquer solutions and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

Pharmaceutical compositions which can be used orally, include push-fit capsules made of gelatin as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules may contain the active ingredients in admixture with filler such as lactose, binders such as starches, lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active ingredients may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for the chosen route of administration.

For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

For administration by nasal inhalation, the active ingredients for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in a dispenser may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The pharmaceutical composition described herein may be formulated for parenteral administration, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. The compositions may be suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.

Pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients may be prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acids esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.

Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use.

The pharmaceutical composition of the present invention may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppository bases such as cocoa butter or other glycerides. Pharmaceutical compositions suitable for use in context of the present invention include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. More specifically, a therapeutically effective amount means an amount of active ingredients (nucleic acid construct) effective to prevent, alleviate or ameliorate symptoms of a disorder (e.g., ischemia) or prolong the survival of the subject being treated.

Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

For any preparation used in the methods of the invention, the therapeutically effective amount or dose can be estimated initially from in vitro and cell culture assays. For example, a dose can be formulated in animal models to achieve a desired concentration or titer. Such information can be used to more accurately determine useful doses in humans.

Toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. The data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage may vary depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl, et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p.1).

Dosage amount and interval may be adjusted individually to provide plasma or brain levels of the active ingredient are sufficient to induce or suppress the biological effect (minimal effective concentration, MEC). The MEC will vary for each preparation, but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. Detection assays can be used to determine plasma concentrations.

Depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.

The amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc.

Compositions of the present invention may, if desired, be presented in a pack or dispenser device, such as an FDA approved kit, which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, for example, may be of labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert. Compositions comprising a preparation of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition, as if further detailed above.

In addition to cell replacement therapy, the embryonic stem cells of the present invention can also be utilized to prepare a cDNA library. mRNA is prepared by standard techniques from the embryonic stem cells and is further reverse transcribed to form cDNA. The cDNA preparation can be subtracted with nucleotides from embryonic fibroblasts and other cells of undesired specificity, to produce a subtracted cDNA library by techniques known in the art.

The embryonic stem cells of the present invention can be used to screen for factors (such as small molecule drugs, peptides, polynucleotides, and the like) or conditions (such as culture conditions or manipulation) that affect the differentiation of lineage precursor to terminally differentiated cells. For example, growth affecting substances, toxins or potential differentiation factors can be tested by their addition to the culture medium.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Maryland (1989); Perbal, “A Practical Guide to Molecular Cloning”,

John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N. Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

Example 1 Generation of Cell Lines Derived from Delayed Blastocyst Culture

Materials and Methods

Blastocyst cultivation: Discarded zygotes were donated by couples undergoing in vitro fertilization (IVF) treatment at Rambam Medical Center having signed consent forms approved by the national Helsinki committee. Zygotes were cultured to the blastocyst stage according to IVF laboratory standard protocol: drops under oil using specialized Cook media (Queensland, Australia) including insemination medium (IM), growth medium (GM) and blastocyst stage embryo medium (BM).

Derivation of extended blastocyst cell (EBC) lines: Following zona pellucida digestion by Tyrode's acidic solution (Sigma Aldrich, St Louis, Mo., USA) the exposed blastocysts were plated on mitotically inactivated mouse embryonic fibroblasts (MEFs). Eight attached blastocysts were cultured on MEFs as whole embryos for 9-14 days post fertilization until a large cyst developed. If needed, due to MEF quality, the embryos were transferred in whole to new MEF-covered plates using 27 gouge syringe needles, leaving a few of the surrounding fibroblasts behind. Following cyst development, a disc-like structure was isolated and plated separately on a fresh MEF-covered plate. Cells with stem cell morphology (small cells with large nucleus) were passaged mechanically. Following a few passages (4-6), when a homogonous culture was achieved, the cells were passaged routinely every four to six days using 1 mg/ml type IV collagenase (Gibco Invitrogen corporation products, San Diago, Calif., USA).

Culture media: For the derivation and initial passages, cells were grown in a culture medium consisting of 80% KO-DMEM and supplemented with 20% defined FBS (HyClone, Utah, USA), 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% non-essential amino acid stock (all from Gibco Invitrogen corporation products, San Diago, Calif., USA products).

The cells were then cultured using medium consisting of 85% ko-DMEM and supplemented with 15% ko-serum replacement, 1 mM L-glutamine, 0.1 mM j3-mercaptoethanol, 1% non-essential amino acid stock and 4 ng/ml basic fibroblast growth factor (bFGF) (all products from Gibco Invitrogen corporation products, San Diago, Calif., USA). The cells were frozen in liquid nitrogen using a freezing solution consisting of 10% DMSO (Sigma, St Louis, Mo., USA), 10% FBS (Hyclone, Utah, USA) and 80% KO-DMEM.

Results

Four EBC lines were derived with the use of the extended blastocyst culture technique. Of the eight plated embryos, four had a surrounding monolayer of trophblast or fibroblast cells, and the inner cell mass (ICM) started to grow as a monolayer, creating a typical ES cell colony following five to ten days (I-5, I-8, I-10, I-11). The other four embryos continued to develop in whole with a notable cyst and a disc-like area (see FIG. 1E) from which the EBC lines were derived (J2, J3, J6, J7). FIGS. 1A-D are photographs of light microscopy images depicting the generation of EBC J3. FIG. 1E is a light microscopy image of the EBC J6.

Example 2 Morphological Analysis of EBCs

Materials and Methods

Karyotype analysis: Cell division was blocked in mitotic metaphase using colcemid-spindle formation inhibitor (karyoMax colcemid solution, Gibco Invitrogen corporation products, San Diago, Calif., USA). Nuclear membranes were broken following hypotonic treatment. For chromosome visualization, G-band standard staining (Giemsa, Merck, Darmstadt, Germany) was performed. The karyotypes were analyzed and reported according to the “International System for Human Cytogenetic Nomenclature” (ISCN). At least 20 cells were examined from each cell line, 10 from each different sample. The samples were taken from the EBCs following at least 20 consecutive passages.

Microscopy: Light microscopy was performed to examine EBC colonies. Electron and monolayer microscopy were performed to examine histological sections of extended blastocyst and embryonic stem cells. The phase-contrast is Olympus CH30, the transmitted electron microscopy in use JEM-100sx (JEOL, Tokyo, Japan).

Results

Karyotype analysis revealed that two of the examined EBC lines comprised a normal 46, XY karyotype and two comprised a normal 46, XX karyotype. None of the 100 cells examined exhibited any karyotype abnormality. The karyotype analysis was carried out following at least 20 passages of continuous culture indicating that the cell lines possess a stable karyotype.

Light microscopy revealed that the colonies formed by the EBCs presented a similar morphology to that of hESC lines i.e. round colonies with spaces between the cells and relatively large nucleii with distinct nucleoli. However, when cell monolayers were examined under a light microscope, it was noted that while the cells inside the EBC colonies were organized as a columnar epithelium with somewhat smaller nucleii and villi throughout the upper side of the colony (FIGS. 2B-C), the ESC colonies were organized as stratified epithelium, with no villi facing the upper side (FIG. 2A). Furthermore, electron microscopy indicated that zonula occludente junctions, typical for columnar epithelium, could be detected between the EBCs and not between the upper rows of hESCs (FIGS. 2D-E). Other reports describe this morphology as the morphology of early differentiating hES cells [Sathananthan et al. 2002].

Example 3 Differentiational Analysis of EBCs Compared to ESCs

Materials and Methods

Immunostaining: EBCs and hESCs were fixed with 4% paraformaldehyde, and exposed to primary antibodies (1:50) overnight at 4° C. Cy3 conjugated antibodies (Chemicon International, Temecula Calif., USA) at a dilution of 1:100 were used as secondary antibodies in combination with all primary antibodies except Brachury where a FITZ conjugated secondary antibody was used (Santa Cruz). Stage-specific embryonic antigens (SSEA) 1,3 and 4 (Hybridoma bank, Iuwa, USA), tumor recognition antigens (TRA) 1-60 and TRA1-81, (Chemicon International, Temecula, Canada) Brachury and Oct4 (Santa Cruz) were used as primary antibodies. For double immunostaining, EBCs and hESCs were fixed with 4% paraformaldehyde, and exposed to Oct4 antibody (1:50) for 30 minutes at room temperature. Following washing, the fixed-cells were incubated for 30 minutes at room temperature with Brachury (1:50) antibody. This protocol was repeated with the secondary antibodies. For each of the reactions a negative control was used in which primary antibodies were not used.

Teratoma formation: 10⁷ cells in 100 μl culture medium were harvested and injected into the rear leg muscles of four-week-old male SCID-beige mice. The resulting teratomas were harvested 9 weeks (±2 days) post injection. Each teratoma was weighed, following which a portion of the tumours was collected for RNA isolation and another portion was fixed. The sections were fixed in 10% neutral-buffered formalin, dehydrated in graduated alcohol (70% -100%) and embedded in paraffin. For histological examination, 1-5 μm sections were deparafinized and stained with hematoxylin/eosin (H&E).

EB formation: For the formation of EBs, four to six confluent wells of a six-well plate (40-60 cm²) of EBCs and hESCs were used. The cells were removed from their culture dishes using 1 mg/ml type IV collagenase, further broken into small clumps using 1000 μl Gilson pipette tips, and cultured in suspension in 58 mm Petri dishes (Greiner, Germany). EBs were grown in suspension for five days in medium supplemented with 15% ko-serum replacement, with similar supplements as the continuous culture medium without the addition of bFGF. After five days in suspension, part of the EBs were trypsinized, further broken up using 1000 μl Gilson pipette tips, and plated on gelatine-coated culture plates. The EB-derived cells were further cultured in medium supplemented with FBS (Hyclone, Utah, USA) for ten to eleven additional days. Both samples of the EBs cultured in suspension and the plated EB-derived cells were collected for RNA isolation.

RT-PCR reaction: Total RNA was isolated from EBCs, five day-old EBs cultured in suspension, plated EB-derived cells and teratoma sections using Tri-Reagent (Sigma Aldrich, St. Louis, Mo., USA), according to the manufacturer's recommended protocol. cDNA was synthesized from 1 μg total RNA using MMLV reverse transcriptase RNase H minus (Promega, Madison, Wis., USA). PCR reactions comprised denaturation for 5 minutes in 94° C. followed by repeated cycles of 30 seconds at 94° C., at the annealing temperature (as in Table 2) and for extension at 72° C. PCR primers and reaction conditions used are as described in Table 2 herein below. PCR products were size fractionated using 2% agarose gel electrophoresis, following staining with ethidium bromide. RT reaction mixture was used as a negative control, and the β-actin gene (a house-keeping gene) was used for normalization.

TABLE 2  Product 5′ primer 3′ primer Mg Annealing Gene size bp SEQ ID NO: SEQ ID NO: mM temp Ref. Undifferentiated markers and receptors Epidermal 300 CAGTCGTCAGCCTG AGGTTGCACTT 1.5  65, Schuldiner et al PNAS growth factor AACATAACATCC GTCCACGCATT AM5 2000 receptor I SEQ ID NO: 1 CCC (EGFR) SEQ ID NO: 2 U48727 U48728 Activin 550 ACACGGGAGTGCA TTCATGAGCTG 1.5 65, Schuldiner et al PNAS receptor β2 TCTACTACAACG GGCCTTCCAGA AM5 2000 (ACTR) SEQ ID NO: 3 CAC AF060200 SEQ ID NO: 4 Octamer 219 GAGAACAATGAGA TTCTGGCGCCG 1.5 55, Abdel-Rahman et al. binding ACCTTCAGGAGA GTTACAGAACC DK4 Hum reprod 1995 protein 4 SEQ ID NO: 5 A (Oct4) SEQ ID NO: 6 NM_00270 Nanog 800 ACTAACATGAGTGT TCATCTTCACAC 1.5 61, Daheron et al Stem NG_004095 GGATCC GTCTTCAG AM1 Cells. 2004 SEQ ID NO: 7 SEQ ID NO: 8 LIF 560 CAGCATCACTGAAT AGTATGAAACA 1.5  61, Chen et al. Fer Ster X13967 CACAGAGC TCCCCACAGGG AM1 1999. SEQ ID NO: 9 SEQ ID NO: 10 LIF-R 459 CAAAAGAGTGTCT CCATGTATTTAC 1.5 61, Chen et al. Fer Ster NM_002310 GTGAG ATTGGC AM1 1999. SEQ ID NO: 11 SEQ ID NO: 12 Rex1 306 GCGTACGCAAATT CAGCATCCTAA 1.5 56, Henderson et al. Stem AF450454 AAAGTCCAGA ACAGCTCGCAG 3AM Cells 2002. SEQ ID NO: 13 AAT SEQ ID NO: 14 FGF4 370 CTACAACGCCTACG GTTGCACCAGA 1.5 52, Henderson et al. Stem NM_002007 AGTCCTACA AAAGTCAGAGT 4AM Cells 2002. SEQ ID NO: 15 TG SEQ ID NO: 16 FGF5 550 CACTGATAGGAAC CTCCGACTGCTT 1.5 65, Crickard et al NM_004464 CCTAGAGG GAATCTTGG AM5 Gynecology Oncology SEQ ID NO: 17 SEQ ID NO: 18 1994 Sox2 448 CCCCCGGCGGCAA TCGGCGCCGGG 1.5 60, Henderson et al. Stem Z31560 TAGCA GAGATACAT DK5 Cells 2002. SEQ ID NO: 19 SEQ ID NO: 20 β-Actin 838 ATCTGGCACCACAC CGTCATACTCCT 1.5 62 Henderson et al. Stem NM_001101 CTTCTACAATGAGC GCTTGCTGATC Cells 2002. TGCG CACATCTGC SEQ ID NO: 21 SEQ ID NO: 22 Retinoic 500 AGCAGCAGTTCTG GTGGAGAGTTC 1.5 65, Schuldiner et al PNAS Acid AAGAGATAGTGCC ACTGAACTTGT AM5 2000 Receptor SEQ ID NO: 23 CCC type alpha SEQ ID NO: 24 (RAR) AH007261 Fibroblast 410 AGCATCATAATGG AGTCCGATAGA 1.5 65, Schuldiner et al PNAS Growth ACTCTGTGGTGCC GTTACCCGCCA AM5 2000 Factor SEQ ID NO: 25 AGC Receptor SEQ ID NO: 26 type I (FGFRI) M34641 Bone 800 TCTGCAGCTAGGTC TATACTGCTCC 1.5 65, Schuldiner et al PNAS Morphogenic CTCTCATCAGC ATATCGACCTC AM5 2000 Protein 4 SEQ ID NO: 27 GGC Receptor SEQ ID NO: 28 type II (BMP4RII) D50516 Hepatocyte 440 AGAAATTCATCAG TTCCTCCGATCG 1.5 65, Schuldiner et al PNAS Growth GCTGTGAAGCGCG CACACATTTGT AM5 2000 Factor SEQ ID NO: 29 CG Receptor SEQ ID NO: 30 (c-Met) AC002080 Nerve 410 TGTTCTCCTGCCAG TCTTGAAGGCT 1.5 65, Schuldiner et al PNAS Growth GACAAGCAGAAC ATGTAGGCCAC AM5 2000 Factor SEQ ID NO: 31 AAGG Receptor SEQ ID NO: 32 (NGFR) AC006487 Transforming 530 TAGTCACTGACAAC ACAGTGCTCGC 1.5 65, Schuldiner et al PNAS Growth AACGGTGCAGTC TGAACTCCATG AM5 2000 Factor SEQ ID NO: 33 AGC Receptor SEQ ID NO: 34 type II (TGFRII) AH004921 Mesodermal markers β-Globulin 410 ACCTGACTCCTGAG TAGCCACACCA 1.5 65, Schuldiner et al PNAS V00499 GAGAAGTCTGC GCCACCACTTT AM5 2000 SEQ ID NO: 35 CTG SEQ ID NO: 36 Collagen 180 CGATGGCTGCACG CAGGTTGGGAT 1.5 64, B. Schmitt et al type 1 α1 AGTCACAC GGAGGGAGTTT AM7 Differentiation 2003 (cartiladge) SEQ ID NO: 37 AC Z74615 SEQ ID NO: 38 Collagen 128 CCGGGCAGAGGGC CAATGATGGGG 1.5 64, B. Schmitt et al type 2 a1 AATAGCAGGTT AGGCGTGAG AM7 Differentiation 2003 (cartiladge) SEQ ID NO: 39 SEQ ID NO: 40 X06268 Cartilage 116 GGGTGGCCGCCTG CTTGCCGCAGC 1.5 64, B. Schmitt et al oligomeric GGGGTCTT TGATGGGTCTC AM7 Differentiation 2003 matrix SEQ ID NO: 41 SEQ ID NO: 42 protein (comp) L32137 Cartilage 145 GCGTCCGCTACCCC GCGCTCTAAGG 1.5 64, B. Schmitt et al link protein ATCTCTA GCACATTCAGT AM7 Differentiation 2003 U43328 SEQ ID NO: 43 T SEQ ID NO: 44 Aggrecan 146 CCAGTGCACAGAG TCCGAGGGTGC 1.5 64, B. Schmitt et al (cartilage) GGGTTTG CGTGAG AM7 Differentiation 2003 X17406 SEQ ID NO: 45 SEQ ID NO: 46 Brachyury 250 TAAGGTGGATCTTC CATCTCATTGGT 2.5 65  P. J. Gokhale et al. Cell NM003181 AGGTAGC GAGCTCCCT AM5 Growth Differ. 2000. SEQ ID NO: 47 SEQ ID NO: 48 Cardiac 630 TCTATGAGGGCTAC CCTGACTGGAA 1.5 65  Schuldiner et al PNAS Actin GCTTTG GGTAGATGG AM5 2000 (cACT) SEQ ID NO: 49 SEQ ID NO: 50 NM_005159 δ-Globin  430 ACCATGGTGCATCT ACTTGTGAGCC 1.5 65  Schuldiner et al PNAS (δ-Glob) GACTCCTGAGG AAGGCATTAGC AM5 2000 V00505 SEQ ID NO: 51 CAC SEQ ID NO: 52 Renin 590 AGTCGTCTTTGACA GGTAGAACCTG 1.5 65  Schuldiner et al PNAS AH007216 CTGGTTCGTCC AGATGTAGGAT AM5 2000 SEQ ID NO: 53 GC SEQ ID NO: 54 GATA4 475 AGACATCGCACTG GACGGGTCACT 1   60, Home Made transcription ACTGAGAAC ATCTGTGCAAC DK5 factor SEQ ID NO: 55 SEQ ID NO: 56 D78260 IL-6 628 ATGAACTCCTTCTC GAAGAGCCCTC 1.5  54.2  Gutsche et al. Mol NM_00060 CACAAGCGC AGGCTGGACTG Human Reproduction SEQ ID NO: 57 SEQ ID NO: 58 2003 BMP2 200 TCAAGCCAAACAC ACGTCTGAACA 1.5 61, Bunger et al. Calcif NM_001200 AAACAGC ATGGCATGA DK3 Tissue Int.2003 SEQ ID NO: 59 SEQ ID NO: 60 BMP4 378 GCCGGAGGGCCAA CTGCCTGATCTC 1.5   64.7, Bae et al. D30751 GCGTAGCCCTAAG AGCGGCACCCA DK2 Toxicological Sciences SEQ ID NO: 61 CATC 2003 SEQ ID NO: 62 CD44 200 CCAACACCTCCCAC TATACTCGCCCT 1.5 61, Ramos-Nino et al. M59040 TATGAC TCTTGCTG DK3 Cancer Research 2003 SEQ ID NO: 63 SEQ ID NO: 64 Endodermal markers Amylase 490 GCTGGGCTCAGTAT GACGACAATCT 1.5 65, Schuldiner et al PNAS M24895 TCCCCAAATAC CTGACCTGAGT AM5 2000 SEQ ID NO: 65 AGG SEQ ID NO: 66 α1 Anti 360 AGACCCTTTGAAGT CCATTGCTGAA 1.5 65, Schuldiner et al PNAS trypsin CAAGGACACCG GACCTTAGTGA AM5 2000 K02212 SEQ ID NO: 67 TGC SEQ ID NO: 68 Albumin 450 CCTTTGGCACAATG CAGCAGTCAGC 1.5 65, Schuldiner et al PNAS M12533 AAGTGGGTAACC CATTTCACCAT AM5 2000 SEQ ID NO: 69 AGG SEQ ID NO: 70 Glucagon 370 CTCAGTGATCCTGA AGTCCCTGGCG 1.5 65, Schuldiner et al PNAS X03991 TCAGATGAACG GCAAGATTATC AM5 2000 SEQ ID NO: 71 AAG SEQ ID NO: 72 α- 216 GCTGGATTGTCTGCA TCCCCTGAAGA 1.5 60, Home made Phetoprotein GGATGGGGAA AAATTGGTTAA DK5 BC027881 SEQ ID NO: 73 AAT SEQ ID NO: 74 GnRH 219 TCAAAAACTCCTAG CTTTCCAGAGC 1.5 55, CTGGCCT TCCTTTCAGGT DK4 SEQ ID NO: 75 SEQ ID NO: 76 CG 556 GCAGCTATCTTTCT ACTCTGAGGTG 2.0 60, GGTCACAT ACGTTCTTTTG DK5 SEQ ID NO: 77 SEQ ID NO: 78 Ectodermal marker Neurofilament 400 TGAACACAGACGC CACCTTTATGTG 1.5 65, Schuldiner et al PNAS heavy Chain TATGCGCTCAG AGTGGACACAG AM5 2000 (NFH) X15307 SEQ ID NO: 79 AG X15309 SEQ ID NO: 80

Chip DNA analysis: Samples of RNA were isolated from confluent cultures of undifferentiated hESCs and EBCs cultured as described in Example 1 with mitotically inactivated MEFs. RNA isolation was conducted as described hereinabove for RT-PCR analysis. Four commercial gene array membranes were used: human stem cell genes, human TGF_(β)/BMP pathway genes, human neurotrophin and receptor genes and extracellular molecules genes (all non-radioactive from GEarray Q series, numbers, HS-018, respectively, SuperArrays Biosciences Inc., Frederick, Md., USA). The analysis was performed according to the supplier's instructions. In brief, for RT reaction 200U Maloney murine leukaemia virus-derived reverse transcriptase was used (Promega, Madisom, Wis., USA). The array membranes were hybridized overnight with biotin-labelled probes at 60° C., washed twice at 60° C. for 15 minutes with 2XSSC/1% SDS followed with 0.1XSSC/1% SDS. The detection stage comprised a 30-minute incubation of the membranes with alkaline phosphatase-conjugated streptavidin followed by a five-minute incubation with CDP-star substrate at room temperature. The membranes were exposed to X-ray film. The quantification of the gene expression was carried out using GEarray analyzer and Scanalyze software.

Real time PCR analysis: cDNA was synthesized as described above for the RT-PCR reaction. Taq-Man Universal PCR master Mix and Assay-on-Demand gene expression Probes for Oct 4 and β-Actin were used according to the manufacturer instructions (Applied Biosystems, Foster City, Calif.). The real time PCR reaction was performed using Applied Biosystem 7000 DNA Sequence Detection system, according to the manufacturer guidelines (Applied Biosystems, Foster City, Calif.). The relative expression of Oct 4 was normalized according to the β-Actin expression in cDNA isolated from the same sample, by using the standard curve method described by the manufacturer. To calculate differences in Oct 4 amplification between the various tested cell lines, a relative standard curve method was used (Applied Biosystems, Foster City, Calif.). The data was collected from three different samples for each line (I3, I6, J3, J6) and each cDNA sample was assayed at least twice, averaged and graphed with standard deviations.

Affymetrix chip analysis: RNA was isolated from undifferentiated I3 cells at passage 45, from I6 cells at passage 42, from J3 cells at passage 37 and from J6 cells at passage 49 following culture on MEFs. RNA integrity was assed by gel electophoresis. Total RNA samples were concentrated at 1 μg/μl, cleaned with Phenol/chlorophorm/Isoamyl alcohol in Phase lock gel (PLG) tubes (Invitrogen Coorperation, San Diego, Calif., USA). 10 μg of each sample was used to prepare biotinylated target cDNA and hybridised to Affymetric focus gene chips according to the manufacturer's instructions. The microarray was scanned by Affymetric scanner (Affymetrix, Santa Clara, Calif., USA). For bioinformatics the MAS 5.0 Affymetrix array analysis software was used. Expression levels of greater than 3 fold were considered relevant. The p-value of each spot was calculated using Anove tests, each SP was centered and normalized. For clustering analysis, the super Paramagnetic Clustering Method was used. David software was used for the Go-Chart analysis.

Illumina beadarray analysis: RNA was isolated from undifferentiated J3 and from hESC as described hereinabove for Affymetrix chip analysis. For gene profiling Illumina Beadarray was used (Sentrix human Expression BeadChip, Illumina, San Diego, Calif., USA).

2-D gel protein electrophoresis analysis: The proteins were dissolved in 150 p1 running buffer consisting of: 7M urea, 2M thiourea, 2% w/v CHAPS, 65 mM DTT and 1.25% v/v ampholyte and 3 β1 Bromo-Phenol-Blue (BPB). The protein levels were measured using the Bradford method. 200 μg of protein were loaded on each strip (BioRad, 3-10 NL, Immobiline DryStrips, 11 cm) and rehydrated for one hour without voltage and subsequently 12 hours in 50 mV. The isoelectric focusing was conducted as follows: one hour in 200 V, 500 V, 1000 V respectively followed by 30 minutes of increased voltage up to 8000 V, where it remained until reaching 69,145 VH on VH (Volt Hours).

Each strip underwent equilibration in 50 mg DTT dissolved in equilibration buffer containing: 6 M Urea, 30% w/v glycerol and 2% SDS in 0.05 M Tris-HCl buffer (1.5 M Tris-HCl and 0.4% w/v SDS), pH 8.8 10 μl BPB, for 15 minutes. The second stage of the equilibration was conducted in 200 mg Iodoacetamide (IAA) dissolved in equilibration buffer and 10 μl BPB, for 15 minutes. The strip were than loaded onto Bio Rad gradient gels (4-20%). A dual color marker was used to evaluate the molecular weight. Electrophoresis was conducted for one hour at 200 V. The resultant gels were stained with SeeBand forte (GeBA) according to the manufacturer's instructions. The gels were scanned using Bio Rad Fluor-S scanner, and analyzed using Bio Rad PDQUEST 7.0.1 software.

Osteoblast differentiation: hESC (I4 and I6) and EBC cells (J3 and J6) were cultured on stromal cell matrix (ATCC no. SR4987) in medium consisting of of 85% MEM alpha, 0.5% Penicillin streptomycin, 0.2% Ribnucleosides & Deoxyribnucleosides (Biological Industries, Bait Haemek, Israel), 15% FBS (HyClonre, Utah, USA), 0.05 mg/ml Ascorbic Acid, 1% β-glycophosphate (Sigma, St. Louis, USA). Following 5 days of co-culture, EBs were formed as described above and cultured in suspension in the identical medium for an additional 5-7 days. The EBs were then dissociated using trypsin-EDTA solution, and re-plated on stromal cell matrix. Following one week, the cells were stained with Alizarin Red (Fluka, Bochs, Switzerland) to identify calcium secretion.

Results:

Based on the morphology of the colonies, it was noted that the background differentiation of the EBCs is higher than that in the regular hESCs. A consistent background differentiation of more than 15% could be detected in the J2 and J6 cell lines. A single-cell clone of the J2 line, J2.1, expressed the same percentage of background differentiation as the parental cell line. The J3 differentiation rates were found to be similar to those of hESCs.

Similar to hESCs, immunostaining of EBCs with embryonic stage-specific markers revealed strong staining with SSEA4 and TRA-1-60, no staining with SSEA1 and weak staining with SSEA3. Unlike hESC, the EBC lines demonstrated weak staining with TRA-1-81 (FIGS. 3A-G).

The teratoma model was used to test the EBC pluripotency. The cells were injected into the hind limb muscles of four-week-old male SCID-beige mice, similar to the method used to assess the pluripotency of hESCs. During the first set of experiments approximately five million cells were injected into each mouse with at least four mice per cell line. This showed a reduced success rate of 30% for the EBCs and a 100% success rate for the hESCs. In order to efficiently compare the pluripotency of the different types of cell lines, the number of injected cells was doubled to ten million per mouse. In this case, 11 of 12 EBC-injected mice resulted in teratomas. The size of the teratomas differed between the two types of cell lines as measured by the tumor weight; specifically the average weight of the hESC-resulting teratomas was 9.4 gr (N=8) and the average weight of the EBC-resulting teratomas was only 3.5 gr (N=12). In addition to the difference in size, the EBC-resulting teratomas contained a limited number of ectoderm and endoderm representative tissues and had a more distinct appearance of mesodermal tissues (FIGS. 4A-B). In one case, the J2 resultant teratoma did not contain any ectodermal tissues (one mouse out of three examined). While screening several teratoma sections, a tissue representative for all three embryonic germ layers could be found (FIGS. 5A-F). In the J6 teratomas, a predominance of cartilage tissues was observed (FIG. 6).

The results from the teratoma experiments give the impression that the EBCs have a higher tendency to differentiate into mesencymal tissue than hESCs. To further confirm this assumption, an in vitro differentiation model was used. Cells from both types were cultured in suspension for 5 days. The resultant EBs were broken into single cells, plated and further cultured for ten additional days as monolayer of differentiating cells. The expression of several genes was compared by RT-PCR between the different cell lines at different differentiation stages.

Several differences between the EBCs and the ESCs were detected in the non-differentiated cells. While the EBCs expressed undifferentiated markers such as OCT4, Nanog, Rex 1 and SOX2, they also expressed some early markers of cartilage differentiation such as COMP, cartilage linked protein and Aggrecan. The hESCs did not express as many differentiation markers at the undifferentiated stage. Another difference was the expression of STAT3 which was highly expressed by the EBCs but was low or non-existent in the hESCs. The results are summarized in Table 3 below.

TABLE 3 Undifferentiated cells I series J series Gene H9 I6 I3 J3 J6 J2 Mesodermal differentiation markers β-Globulin − + + + − − Collagen type I − + + + + + COMP (Cartilage) −− −− −− +− ++ ++ Collagen type II − − − + + + Cartilage link protein − − − + + + Aggrecan − − − + + + Cardiac actin (cACT) − − + + + + δ-Globulin + − + − − − Renin + − + + + + Brachychyury −− −− −− −+ ++ ++ BMP 4 − − − + + + BMP2 −+ −+ −+ ++ ++ ++ Endodermal differentiation markers Amylase + + + − + − α1 Anti trypsin + − + + + + Albumin + + + − − − Glucagon − − − − − − GnRH + + + + + + CGα + + + − − + Ectodermal differentiation marker Neurofilament heavy − − + + + + chain (NFH) Undifferentiated cell markers and receptors Epidermal GF receptor I ++ ++ ++ +− ++ ++ (EGERI) Activin receptor β2 − − − + + + Retinoic acid receptor + + + + + + type α (RAR) Fibroblast GF receptor + + + + + + (FGFRI) BMP4RII + − − + + − Hepatocyte GF receptor + + + + + + C-Met Nerve GF receptor − − − + + + NGFR Transforming GF receptor II + + + + + + (TGF) Oct 4 + + + + + + Rex 1 ++ ++ ++ ++ ++ ++ Nanong +++ +++ +++ ++− ±++ ++− FGF4 ++− ++− +++ −−− −+− +++ Sox2 −++ +−+ +++ +++ +++ −++

To evaluate possible differences in Oct 4 expression between EBCs and hESCs, a real time PCR analysis was conducted. Although the RT-PCR reaction revealed a clear band for Oct 4 expression for the EBC cells, according to quantitative real-time PCR analysis the levels of Oct 4 expression in these cells is significantly lower compared with hESCs (FIG. 7).

To allow a wider comparison between the two cell types, commercial DNA chip analysis was performed using an array of 288 “stem cells genes” (FIGS. 8A-D). When the number of genes with significant expression differences between two different hESC lines and two separate EBC lines were compared, only minor differences were found of 15 and 9 genes, respectively. When the genes' expression pattern was compared between the average of the EBC lines and hESC lines, 90 genes demonstrated different expression levels. Most of these genes had statistically higher expression in the EBCs—these genes are summarized in Table 4 hereinbelow.

TABLE 4 Confirmed I series J series by Gene I6 I3 H9 J2 J6 J3 RT-PCR Bone morphogenetic protein +− ND +− ++ ++ ND + 2 (BMP2) NM_001200 Bone morphogenetic protein − ND − + + ND + 4 (BMP4) NM_001200 CD44 Antigen M59040 − ND − + + ND + Cadherin 3 placental (CDH3) −+ ND −+ ++ ++ ND NM_001793 GATA4 transcription factor − ND − + + ND + D78260 Growth differentiation factor − ND − + + ND 3 (GDF3) NM_020634 Interleukin 6 (IL6) − ND − + + ND + NM_00060 Integrin beta 5 (ITGB5) − ND − + + ND NM_002213 Leukemia inhibitory factor − ND − + + ND + (LIF) X13967 Nerve growth factor − ND − + + ND beta polypeptide (NGFB) X52599 NK2 homolog B (NKX2B) − ND − + + ND NM_002509 Hypothetical protein −+ ND −+ ++ ++ ND (FLJ10314) BC039861 Noggin (NOG) NM_005450 − ND − + + ND Notch homolog 1translesion − ND − + + ND associated (NOTCH1) AF308602 Patched homolog − ND − + + ND (PTCH) U43148 Sox 13 SRY box 13 (SOX13) − ND − + + ND NM_005686 Sox18 SRY box 18 (Sox 18) − ND − + + ND NM_018419 Sox 2 SRY box 2 (Sox 2) − ND −+ + + ND −+ BC013923 Transforming growth factor −+ ND −+ ++ ++ ND beta receptor III (TGFBR3) NM_003243 THY-1 cell surface antigen − ND − ++ ++ ND (THY1) NM_006288 Undifferentiated − ND − + −+ ND embryonic cell transcription factor 1 (UTF1) NM_003577 Wingless-type MMTV − ND − + + ND integration family 6 (WNT6) NM_006522 Zinc finger protein 42 − ND − + + ND (ZFP42) AK056719

Among these genes it was found that BMP2 expression was higher in the undifferentiated EBCs and mesencymal markers such as BMP4, CD44, GATA4 (known also as early endodermal marker) were expressed by the two examined EBC lines. The expression of these genes was further confirmed by RT-PCR.

Table 5 below summarizes the results of TGF_(β)related gene expression as analyzed by chip analysis.

TABLE 5 Confirmed I series J series by Gene I6 I3 H9 J2 J6 J3 RT-PCR Bone morphogenetic − ND ND ND +/− ND + protein 2 (BMP2) NM_001200 Bone morphogenetic − ND ND ND ++ ND + protein 4 (BMP4) NM_001200 Anti Mullerian −/+ ND ND ND ++ ND hormone (AMH) NM_000479 Anti Mullerian + ND ND ND + ND hormone receptor type II (AMHR2) NM_020547 Bone morphogenetic − ND ND ND + ND protein 6 (BMP6) NM_001718 Bone morphogenetic − ND ND ND +/− ND protein receptor type IA (BMPR1A) NM_004329 Bone morphogenetic − ND ND ND +/− ND protein receptor type 2 (BMPR2) Z48923 Cyclin dependent −/+ ND ND ND + ND kinase inhibitor 1A (CDKN1A) L47233 Cerberus 1 (CER1) ++ ND ND ND ++ ND NM_005454 Collagen type I ++ ND ND ND ++ ND alpha2 (COL1A2) NM_000089 Collagen type III ++ ND ND ND ++ ND alpha1 (COL3A1) NM_000090 Distal-less homeo − ND ND ND ++ ND box 2 (DLX2) NM_004405 Lefty A +++ ND ND ND +++ ND (endometrial bleeding associated factor) (EBAF) NM_003240 Bone morphogenetic ++ ND ND ND ++ ND protein 9 = growth differentiation factor 2 (BMP9) AF188285 Growth differentiation − ND ND ND + ND factor 5 (GDF5, = cartilage derived morphogenetic protein 1) NM_000557 DNA-binding protein −/+ ND ND ND ++ ND inhibitor ID-1 (ID1) D13889 Inhibitor of DNA + ND ND ND +++ ND binding 2, dominant negative helix-loop- helix protein (ID2) D13891 Inhibitor of DNA −/+ ND ND ND ++ ND binding 3, dominant negative helix-loop- helix protein (ID3) X66924 Inhibitor of DNA +++ ND ND ND +++ ND binding 4, dominant negative helix-loop- helix protein (ID4) NM_001546 Inhibin α (INHA) +++ ND ND ND +++ ND NM_002191 Jun B proto- + ND ND ND + ND oncogene (JUNB) X51345 Lefty B (LEFTB) +++ ND ND ND +++ ND NM_020997 MAD homolog 2 −/+ ND ND ND ++ ND (MADH2) NM_005901 MAD homolog 3 −/+ ND ND ND ++ ND (Smad 3) NM_005902 MAD homolog 6 ++ ND ND ND ++ ND (Smad 6) NM_005585 v-myc avian − ND ND ND ++ ND myelocytomatosis viral oncogene homolog (c-myc) X00364 Runt-related ++ ND ND ND ++ ND transcription factor 2 (RUNX2) L40992 Plasminogen activator +++ ND ND ND +++ ND inhibitor type I (SERPINE1) M16006 Homo sapiens −/+ ND ND ND + ND teratocarcinoma- derived growth factor 1 (TDGF1) NM_003212 Transforming growth −/+ ND ND ND +++ ND factor beta 1 (TGF_(β1)) X02812 TGF_(β) induced factor − ND ND ND ++ ND (TGIF) NM_003244 Tissue inhibitor of − ND ND ND ++ ND metalloproteinase 1 (TINP1) (erythroid potentiating activity, collagenase inhibitor) NM_003254 Transforming growth − ND ND ND ++ ND factor beta stimulated protein (TSC22) NM_006022

Table 6 summarizes the data accumulated following chip analysis of all Extracellular Matrix related genes.

TABLE 6 Confirmed I series J series by Gene I6 I3 H9 J6 J2 J3 RT-PCR Caveolin 1, + ND ND + ND ND Cavaolae protein 22 KD (CAV1) NM_001753 Cadherin 1, Type 1 ++ ND ND ++ ND ND epithelial Cadherin (CDH1) Z13009 Carcinoembryonic ++ ND ND ++ ND ND antigen-related cell adhesion molecule 5 (CEACAM5) NM_004363 Collagen type XVIII ++ ND ND +/− ND ND (Endostatin) AF018081 Collagen type 1 ++ ND ND + ND ND alpha 1 (Col1 A1) NM_000088 Collagen type IV ++ ND ND + ND ND alpha 2 (Col4A2) X05610 Cystatin C (amyloid ++ ND ND + ND ND anglopathy and cerebral hemorrhage, CST3) NM_000099 Catenin, Cadherin ++ ND ND + ND ND associated protein, alpha 1 (CTNNA1) NM_001903 Catenin, Cadherin ++ ND ND + ND ND associated protein, Beta 1 (CTNNB1) NM_001904 Catenin, Cadherin ++ ND ND ++ ND ND associated protein, delta 1 (CTNND1) AF062343 Cathepsin B (CTSB) ++ ND ND + ND ND L16510 Cathepsin D + ND ND − ND ND lysosomal aspartyl protease (CTSD) M11233 Cathepsin L ++ ND ND + ND ND (CTSL) X12451 Fibronectin 1 +++ ND ND +++ ND ND (FN1) X02761 Integrin alpha 5, +++ ND ND −/+ ND ND fibronectin receptor (ITGA5) X06256 Integrin alpha 6, −/+ ND ND − ND ND laminin receptor (ITGA6) X53586 Integrin alpha V, +++ ND ND +++ ND ND vitronectin receptor (ITGAV) NM_002210 Integrin beta 1, +++ ND ND +++ ND ND fibronectin receptor (ITGB1) NM_002211 Integrin beta 5, +++ ND ND +++ ND ND (ITGB5) J05633 Laminin B1 chain +++ ND ND +++ ND ND (LAMB1) M61916 Laminin gamma 1 + ND ND − ND ND (LAMC1) Jo3202 Hyaluronidases, +++ ND ND + ND ND meningioma expressed antigen 5 (MGEA5) NM_012215 Matrix ++ ND ND − ND ND Metalloproteinase 1 (MMP1) X05231 Matrix ++ ND ND − ND ND Metalloproteinase 10 (MMP10) NM_002425 Stromelysin-3 + ND ND − ND ND (MMP11) X57766 Matrix + ND ND − ND ND Metalloproteinase 13 (MMP13) X75308 mRNA for +++ ND ND −/+ ND ND membrane type matrix Metalloproteinase 1 (MMP14) D26512 Matrix +++ ND ND − ND ND Metalloproteinase 15 membrane inserted (MMP15) D86331 Matrix + ND ND − ND ND Metalloproteinase 17 membrane inserted (MMP17) NM_016155 Matrix +++ ND ND +++ ND ND Metalloproteinase 2 (MMP2) J03210 Matrix +++ ND ND −/+ ND ND Metalloproteinase 24 membrane inserted (MMP24) NM_006690 mRNA matrix +++ ND ND +++ ND ND Metalloproteinase 26 (MMP26) AF291664 Matrix +++ ND ND − ND ND Metalloproteinase 3 (MMP3) X05232 Neurophil cell + ND ND − ND ND adhesion molecule (NRCAM) NM_005010 Plasminogen +++ ND ND +++ ND ND activator inhibitor type 1 (SERPINE1) M16006 Osteonectin, +++ ND ND +++ ND ND secreted protein acidic cystein-rich (SPARC) XM_003989 Osteopontin, +++ ND ND +++ ND ND secreted phosphoprotein 1 (SPP1) M83248 Thrombosponin 1 +++ ND ND +++ ND ND (THBS1) NM_003246 Tissue inhibitor of +++ ND ND −/+ ND ND metalloproteinase 1 (TIMP1) NM_003254 Tissue inhibitor of +++ ND ND ++ ND ND metalloproteinase 2 (TIMP2) NM_003255 Tissue inhibitor of ++ ND ND −/+ ND ND metalloproteinase 3 (TIMP3) NM_000362

Table 7 summarizes the data accumulated following chip analysis of all LIF pathway related genes.

TABLE 7 Confirmed I series J series by Gene I6 I3 H9 J6 J2 J3 RT-PCR BCL2-associated X + ND ND + ND ND protein (Bax) L22474 Cerebellin 1 + ND ND + ND ND precursor (CBLN1) NM_004352 Corticotropin releasing + ND ND + ND ND hormone (CRH) NM_000756 Corticotropin releasing −/+ ND ND + ND ND hormone binding protein (CRHBP) NM_001882 Corticotropin releasing ++ ND ND ++ ND ND hormone receptor 1 (CRHR1) NM_004382 Corticotropin releasing ++ ND ND +++ ND ND hormone receptor 2 (CRHR2) NM_001883 Chemokine receptor 4 + ND ND + ND ND (CXCR4) NM_003467 Prothrombin kringle-1 + ND ND + ND ND (F2) J00307 Basic fibroblast −/+ ND ND −/+ ND ND growth factor (FGF2) NM_002006 Fibroblast growth + ND ND + ND ND factor 9 (FGF9) XM_007105 Fibroblast growth + ND ND + ND ND + factor receptor 1 (FGFR1) M34185 Fusion derived from + ND ND ++ ND ND t(12; 16) malignant liposarcoma (FUS) NM_004960 Heat shock 27 KD + ND ND + ND ND protein (HSPB1) Z23090 Interleukin 6 (IL6) − ND ND −/+ ND ND M14584 Interleukin 6 signal + ND ND + ND ND transducer, gp130 oncostatin M receptor (gp130) NM_002184 v-jun avian sarcoma ++ ND ND +++ ND ND virus 17 oncogene homolog (v-jun) NM_002228 Leukemia inhibitory + ND ND + ND ND + factor receptor mRNA (LIFR) NM_002310 Leukemia inhibitory − ND ND − ND ND Was factor (LIF) X13967 demonstrated with RT- PCR for J6 Neurotrophin + ND ND + ND ND receptor-interacting MAGE homologue (MAGED1) NM_006986 Nerve growth factor + ND ND + ND ND beta polypeptide (NGFB) X52599 Neuropeptide Y + ND ND + ND ND receptor Y6 (NPY6R) NM_006173 Suc1-associated + ND ND + ND ND neurotrophic factor target 2 (FGFR signaling adaptor) (SNT-2) NM_006653 Signal transducer −/+ ND ND ++ ND ND and activator of transcription 3 (STAT3) NM_003150 Tumor protein P53 −/+ ND ND + ND ND (p53) M14694 Urocortin (UCN) ++ ND ND +++ ND ND NM_003353

The difference between EBC and hESC gene expression could be the result of either the higher background differentiation of the EBCs compared to that of the hESCs, as mentioned earlier, or a significant difference between the two cell lines stemming from the different embryonic developmental stage. To explore the two possibilities, double staining for OCT4 and early mesodermal marker—Brachyury [Herrmann et al. 1990; Wilkinson et al. 1990; Herrmann 1991] was performed. It was hypothesized, that if the difference was due to background differentiation, then in some colonies only several EBCs would be positive for Brachyury and that these cells would be negative for OCT4. A double expression of the two markers would indicate that the second possibility is more likely to be true. First, the expression of Brachyury was measured in undifferentiated cells by RT-PCR. Only line J6 expressed this gene in three separate samples, whereas J2 and J3 expressed it inconsistently. The hESCs did not express it in any of the examined nine samples from three different lines. No double staining was found in undifferentiated colonies of the hESC line I3. It was found that almost all the cells were positive for OCT4 and few were positive for Brachyury (FIGS. 9A-I). However, when undifferentiated colonies of the line J6 were examined, most of the cells were double stained (FIGS. 10A-I).

The gene profiles of undifferentiated hES cells from lines I3 and I6, and undifferentiated EB cells from lines J3 and J6 were compared using Affimetrix focused DNA chips (Affymetrix U133A GeneChip DNA microarray). Clustering analysis of the four lines showed a distinct expression (FIGS. 11A-B). Lines I3 and I6 exhibited a significantly higher number of “present” calls (According to the MASS method of analysis, “present” call genes are those whose 11 representative expression spots averaged a score higher than 30) than J3 and J6. No differences were found between the number of “present” calls of I3 compared with I6, or J3 compared with J6, although some individual gene expression signals were found to be different. This finding is consistent with other reports demonstrating that embryonic stem cells express a higher number of genes compared with other progenitors (such as hematopoietic stem cells or skin stem cells); these genes “switch off” during the differentiation process [Mashiach et al, 2005, FASEB 19:147-9]. The signal intensities of lines J3 and J6, however, were found to be higher than the signal intensities produced by the hESC lines. A list of 238 genes in lines J3 and J6 was found to be significantly different (either increased or decreased three fold) than the average expression of I3 and I6 as examined by t-test. The gene list also includes the early mesodermal marker Brachyury, further corroborating both the RT-PCR results and the double staining with Oct 4. Go-chart analysis of these 238 genes revealed that the majority of these genes are related to cell growth, cell maintenance, metabolism of proteins and nucleic acid and signal transduction pathways (FIG. 12). The signal transduction genes include 4 genes from the WNT signaling pathway, which were found to be decreased in line J3 and J6.

To allow an even wider comparison between the two cell types, illumine bead array analysis was performed using an array of 24,364 genes. The results are summarized in Table 8 below (J3—cells of the present invention; hES-human embryonic stem cells; Shh—Chip control; sd—standard deviation; av—average). It was found that 2498 of them showed a 5 fold change in expression level. Of these, only 696 genes (27%) were expressed at a higher level (greater than 5 fold) in the stem cells of the present invention. The average expression level of those 696 genes was much lower than the average expression level of those genes where expression was higher in ESCs than the stem cells of the present invention. The same result appears when expression changes by at least 15 fold is examined; 1354 genes are expressed in the hESC while only 411 (30%) in the DBC cells.

Lengthy table referenced here US20130108597A1-20130502-T00001 Please refer to the end of the specification for access instructions.

Using two-dimensional gel electrophoresis, extracted proteins from undifferentiated cells, and 5-day-old EBs from I6, I4, J3 and J6 lines were compared. Clear differences were found between the treatments (FIGS. 13A-B). More differences were found between the EBs derived from EBCs compared with corresponding undifferentiated EBCs than the EBs derived from hESCs compared with corresponding undifferentiated ESCs. These differences include both protein appearance and post translational differences such as phosphorylation.

Directed differentiation into osteoblasts was also tested. These experiments revealed higher staining of calcium in EBs derived from EBCs compared with EBs to derived from hESCs. Examples are illustrated in FIG. 14.

CONCLUSIONS

Like hESCs, EBCs sustain a normal karyotype, express most of the typical ES cell surface markers, are capable of undifferentiated prolonged proliferation and demonstrate the ability to differentiate into the three embryonic germ layers progeny.

On the other hand, EBCs hold a significantly different genetic signature, including expressing early mesodermal markers at the undifferentiated stage, demonstrating a tendency to differentiate into mesodermal tissues, having an altered expression profile, having a lower tendency to form teratomas, having an altered single cell and colony morphology, and having a reduced pluripotency in comparison with hESCs.

It appears that EBCs represent a distinct cell-population related to early stage of embryonic development, as compared to hESCs.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination.

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims. All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention.

LENGTHY TABLES The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20130108597A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3). 

What is claimed is:
 1. A method of generating a lineage specific cell comprising inducing a lineage-specific cell differentiation in an isolated primate embryonic cell, wherein said isolated primate embryonic cell line exhibits for at least 20 passages an undifferentiated proliferative state, the ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue and a double staining expression of brachyury and Octamer binding transcription factor 4 (OCT-4), but not of SSEA-1, thereby generating the lineage specific cell.
 2. The method of claim 1, wherein said isolated primate embryonic cell line further expresses at least one cartilage marker.
 3. The method of claim 2, wherein said at least one cartilage marker is selected from the group consisting of COMP, aggrecan and collagen type II.
 4. The method of claim 1, wherein said isolated primate embryonic cell line maintains a stable normal karyotype for at least one year.
 5. The method of claim 1, wherein said isolated primate embryonic cell line expresses SSEA4 and TRA-1-60 markers.
 6. The method of claim 1, wherein said isolated primate embryonic cell line expresses less TRA-1-81 marker than an embryonic stem cell of the same primate species not expressing brachyury using identical assay conditions.
 7. The method of claim 1, wherein said isolated primate embryonic cell line is capable of colony organization of columnar epithelium with villi throughout the upper side of said colony.
 8. The method of claim 1, wherein said isolated primate embryonic cell line exhibits an OCT4 protein level lower than the OCT4 protein level in an embryonic stem cell of the same primate species not expressing brachyury using identical assay conditions.
 9. The method of claim 1, wherein said isolated primate embryonic cell line expresses more mesodermal differentiating markers than an embryonic stem cell of an identical primate not expressing brachyury using identical assay conditions.
 10. The method of claim 1, wherein said isolated primate embryonic cell line being genetically modified.
 11. The method of claim 1, wherein said inducing is effected in vitro.
 12. The method of claim 1, wherein said inducing is effected ex-vivo.
 13. The method of claim 1, wherein said lineage-specific cell comprises cardiomyocytes.
 14. The method of claim 1, wherein said lineage-specific cell comprises neural or glial lineages
 15. The method of claim 1, wherein said lineage-specific cell comprises hematopoietic cells.
 16. The method of claim 1, wherein said lineage-specific cell comprises insulin-secreting beta cells.
 17. The method of claim 1, wherein said differentiation is directed by genetic modification.
 18. The method of claim 1, wherein said differentiation comprises formation of embryoid bodies.
 19. The method of claim 1, wherein said primate is a human.
 20. A method of treating or preventing a disease in which cell transplantation is therapeutically beneficial comprising; (a) inducing cell differentiation in an isolated human embryonic cell line, wherein said isolated human embryonic cell line exhibits for at least 20 passages an undifferentiated proliferative state, the ability to differentiate to derivatives of each of an endoderm, mesoderm, and ectoderm tissue and a double staining expression of brachyury and Octamer binding transcription factor 4 (OCT-4), but not of SSEA-1; and (b) transplanting a therapeutically effective amount of the differentiated cells into a subject in need thereof, thereby preventing or treating a disease in which cell transplantation is therapeutically beneficial.
 21. The method of claim 20, further comprising genetically modifying the differentiated cell to express a therapeutic agent.
 22. The method of claim 20, wherein said inducing cell differentiation comprises genetically modifying a plurality of said cells. 